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- PDB-2hkm: Crystal structure of the Schiff base intermediate in the reductiv... -

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Basic information

Entry
Database: PDB / ID: 2hkm
TitleCrystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with phenylethylamine.
Components(Aromatic amine dehydrogenaseAralkylamine dehydrogenase (azurin)) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


aralkylamine dehydrogenase (azurin) / aralkylamine dehydrogenase (azurin) activity / amine dehydrogenase activity / amine metabolic process / periplasmic space
Similarity search - Function
Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase ...Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-PHENYLETHYLAMINE / Aralkylamine dehydrogenase light chain / Aralkylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsRoujeinikova, A. / Leys, D.
CitationJournal: To be Published
Title: Structure-reactivity correlations and kinetic isotope effects in aromatic amine dehydrogenase
Authors: Hothi, P. / Roujeinikova, A. / Sutcliffe, M.J. / Cullis, P. / Leys, D. / Scrutton, N.S.
History
DepositionJul 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Aromatic amine dehydrogenase
H: Aromatic amine dehydrogenase
A: Aromatic amine dehydrogenase
B: Aromatic amine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5056
Polymers109,2604
Non-polymers2442
Water23,0951282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-34 kcal/mol
Surface area31910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.398, 89.109, 80.082
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number4
Space group name H-MP1211
Detailsthe asymmetric unit contains the biological unit, (alpha)2(beta)2 tetramer

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Components

#1: Protein Aromatic amine dehydrogenase / Aralkylamine dehydrogenase (azurin)


Mass: 14516.898 Da / Num. of mol.: 2 / Fragment: AADH subunit alpha (residues 73-433) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P84887, EC: 1.4.99.4
#2: Protein Aromatic amine dehydrogenase / Aralkylamine dehydrogenase (azurin)


Mass: 40113.238 Da / Num. of mol.: 2 / Fragment: AADH subunit beta (residues 48-182) / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: IFO 14479 / References: UniProt: P84888, EC: 1.4.99.4
#3: Chemical ChemComp-PEA / 2-PHENYLETHYLAMINE / Phenethylamine


Mass: 122.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1282 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 2000 MME, AMMONIUM SULPHATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.3→52.632 Å / Num. obs: 155952 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 5
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.5 / Num. measured all: 76282 / Num. unique all: 22949 / Rsym value: 0.42 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.315 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 7817 5 %RANDOM
Rwork0.159 ---
all0.161 155862 --
obs-155862 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0.28 Å2
2---0.09 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7351 0 18 1282 8651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217614
X-RAY DIFFRACTIONr_bond_other_d0.0010.026586
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.93810348
X-RAY DIFFRACTIONr_angle_other_deg0.734315381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2945951
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87624.143350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.629151213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7471543
X-RAY DIFFRACTIONr_chiral_restr0.0820.21116
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021539
X-RAY DIFFRACTIONr_nbd_refined0.1980.21356
X-RAY DIFFRACTIONr_nbd_other0.1960.27056
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23691
X-RAY DIFFRACTIONr_nbtor_other0.0970.24381
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2988
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.252
X-RAY DIFFRACTIONr_mcbond_it2.2144.54995
X-RAY DIFFRACTIONr_mcbond_other0.7134.51952
X-RAY DIFFRACTIONr_mcangle_it2.66867655
X-RAY DIFFRACTIONr_scbond_it4.01393199
X-RAY DIFFRACTIONr_scangle_it5.172122690
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 582 -
Rwork0.231 10978 -
obs-11560 99.84 %

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